Detailed view for PVX_122275

Basic information

TDR Targets ID: 265710
Plasmodium vivax, mRNA-decapping enzyme 2, putative
Source Database / ID:  PlasmoDB 

pI: 9.1005 | Length (AA): 1420 | MW (Da): 158695 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG5

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00293   NUDIX domain
PF05026   Dcp2, box A domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030145   manganese ion binding  
GO:0016787   hydrolase activity  
GO:0003723   RNA binding  

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 9 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
43 297 2a6t (A) 6 243 38.00 0 1 0.52 -0.31
123 263 1f3y (A) 4 165 23.00 0 1 -0.03 0.68
136 265 1ktg (A) 3 137 18.00 0 1 0.2 -0.81
51 311 2qkm (B) 14 262 38.00 0 1 0.616403 -0.2
135 271 4kg3 (A) 102 238 42.00 0.0000016 1 0.722479 -1.5
136 284 4kg3 (A) 103 239 42.00 0 1 0.61763 -0.95
144 268 4mpo (G) 18 148 23.00 0.000000015 0.98 0.365728 -0.02
148 261 4mpo (A) 26 141 30.00 0.00049 1 0.249882 0.73
160 262 3fjy (A) 55 183 33.00 0.15 0.24 0.179135 1.2

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_128366)

Species Accession Gene Product
Arabidopsis thaliana AT5G13570   mRNA-decapping enzyme subunit 2
Babesia bovis BBOV_III003580   hydrolase, NUDIX family protein
Brugia malayi Bm1_26285   Dcp2, box A domain containing protein
Candida albicans CaO19.13730   mRNA decapping
Candida albicans CaO19.6373   mRNA decapping
Caenorhabditis elegans CELE_F52G2.1   Protein DCAP-2, isoform B
Cryptosporidium hominis Chro.70307   hypothetical protein
Cryptosporidium parvum cgd7_2710   ataxin2 related nudix domain protein (RNA processing phosphatase/ATpase domain)
Dictyostelium discoideum DDB_G0283315   mRNA-decapping enzyme 2
Drosophila melanogaster Dmel_CG6169   Decapping protein 2
Echinococcus granulosus EgrG_000591100   mRNA decapping enzyme 2
Entamoeba histolytica EHI_098250   mutT/nudix family protein
Entamoeba histolytica EHI_058810   mRNA decapping protein, putative
Echinococcus multilocularis EmuJ_000591100   mRNA decapping enzyme 2
Homo sapiens ENSG00000172795   decapping mRNA 2
Mus musculus ENSMUSG00000024472   DCP2 decapping enzyme homolog (S. cerevisiae)
Neospora caninum NCLIV_045720   mRNA decapping protein, putative
Oryza sativa 4331069   Os02g0805900
Plasmodium berghei PBANKA_1407400   mRNA-decapping enzyme 2, putative
Plasmodium falciparum PF3D7_1308900   mRNA-decapping enzyme 2, putative
Plasmodium knowlesi PKNH_1409300   mRNA-decapping enzyme 2, putative
Plasmodium vivax PVX_122275   mRNA-decapping enzyme 2, putative
Plasmodium yoelii PY07320   NUDIX domain, putative
Saccharomyces cerevisiae YNL118C   Dcp2p
Schistosoma japonicum Sjp_0302680   ko:K01567 DCP2 decapping enzyme homolog [EC:3.-.-.-], putative
Schistosoma mansoni Smp_006190   hypothetical protein
Schmidtea mediterranea mk4.014035.02  
Schmidtea mediterranea mk4.005775.00  
Schmidtea mediterranea mk4.011103.01  
Schmidtea mediterranea mk4.016861.00  
Schmidtea mediterranea mk4.000160.05  
Schmidtea mediterranea mk4.000160.02  
Toxoplasma gondii TGME49_227450   hydrolase, NUDIX family protein
Theileria parva TP03_0049   hypothetical protein
Trichomonas vaginalis TVAG_198330   mRNA decapping protein, putative

Essentiality

PVX_122275 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F52G2.1 Caenorhabditis elegans embryonic lethal wormbase
YNL118C Saccharomyces cerevisiae inviable yeastgenome
TGME49_227450 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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Gene identifier PVX_122275 (Plasmodium vivax), mRNA-decapping enzyme 2, putative
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